Contacts of the helix formed by residues 579 - 590 (chain B) in PDB entry 1XMI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 579 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B LEU* 1.3 75.8 - - - +
580B VAL* 1.3 64.6 + - - +
581B LEU* 3.2 21.1 + - - +
582B THR* 2.5 28.2 + - - -
583B GLU* 3.1 21.6 + - - +
661B ILE* 3.8 19.4 - - + +
664B GLU* 3.3 22.1 - - - +
665B THR* 3.5 26.0 + - - +
668B ARG* 3.3 19.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B ASP* 1.3 73.7 - - - +
581B LEU* 1.3 63.5 + - + +
583B GLU* 3.7 13.1 - - - +
584B LYS* 3.0 56.4 + - + +
606B LYS* 5.9 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 581 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B ASP* 3.2 9.9 + - - +
580B VAL* 1.3 79.3 - - + +
582B THR* 1.3 60.8 + - - +
584B LYS* 3.4 23.3 + - + +
585B GLU* 3.1 33.2 + - - +
668B ARG* 3.6 34.3 - - - +
669B PHE* 5.3 12.8 - - + -
450C ARG* 5.7 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 582 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B GLN* 3.8 11.0 - - - +
555B ARG* 4.6 2.0 - - - +
578B LEU* 4.0 15.5 - - + -
579B ASP* 2.5 29.5 + - - -
581B LEU* 1.3 73.3 - - - +
583B GLU* 1.3 65.8 + - - +
585B GLU* 3.3 3.4 + - - +
586B ILE* 2.9 45.4 + - + +
664B GLU* 4.6 1.3 - - - +
667B ARG* 3.6 26.8 + - - +
668B ARG* 3.1 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 583 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B PHE* 3.2 44.3 - - + +
578B LEU* 4.1 17.8 - - + +
579B ASP 3.1 16.3 + - - +
580B VAL* 3.7 14.4 - - - +
582B THR* 1.3 77.1 - - - +
584B LYS* 1.3 57.7 + - + +
586B ILE* 3.8 0.5 - - - +
587B PHE* 2.9 30.3 + - - +
604B THR* 5.2 0.2 + - - -
606B LYS* 3.6 31.1 + - - +
609B HIS* 3.4 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 584 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B VAL* 3.0 40.6 + - + +
581B LEU* 3.6 23.0 - - + +
582B THR 3.3 0.2 - - - -
583B GLU* 1.3 78.1 - - + +
585B GLU* 1.3 62.4 + - + +
587B PHE* 3.6 8.0 + - - +
588B GLU* 3.2 23.2 + - - +
608B GLU* 3.4 37.2 + - + +
609B HIS* 5.5 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 585 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B GLN* 2.9 26.9 + - - +
581B LEU* 3.1 14.6 + - - +
582B THR* 3.3 2.2 + - - +
584B LYS* 1.3 78.6 - - + +
586B ILE* 1.3 58.2 + - - +
588B GLU* 3.4 6.4 + - - +
589B SER* 2.9 30.8 + - - -
668B ARG* 2.6 48.7 + - - -
450C ARG* 3.7 18.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B ALA 4.0 12.3 - - - +
524B CYS* 3.8 9.0 - - - +
525B GLN* 4.0 17.0 - - + +
555B ARG* 3.6 36.3 - - + -
558B LEU* 3.7 30.5 - - + -
575B PHE* 3.9 8.7 - - + -
578B LEU* 4.0 8.1 - - + -
582B THR* 2.9 31.1 + - + +
583B GLU 4.2 1.8 - - - +
585B GLU* 1.3 72.6 - - - +
587B PHE* 1.3 61.2 + - - +
588B GLU 3.1 1.3 - - - -
589B SER* 3.5 4.5 - - - -
590B CYS* 2.8 43.2 + - + +
591B VAL* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 587 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B LEU* 4.4 5.8 - - + -
575B PHE* 4.1 13.2 - + + -
583B GLU 2.9 19.2 + - - +
584B LYS* 3.8 7.0 - - - +
586B ILE* 1.3 75.8 - - - +
588B GLU* 1.3 61.8 + - + +
591B VAL* 3.2 27.9 + - + +
592B CYS* 2.9 48.7 + - - -
602B LEU* 3.7 26.5 - - + -
608B GLU* 4.4 7.2 - - + -
609B HIS* 3.5 53.6 - + + +
612B LYS* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 588 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B LYS 3.2 18.4 + - - +
585B GLU* 3.5 6.3 - - - +
586B ILE 3.1 0.4 - - - -
587B PHE* 1.3 77.5 - - + +
589B SER* 1.3 60.9 + - - +
592B CYS* 3.3 15.9 - - - +
593B LYS* 3.0 70.0 + - - +
612B LYS* 3.8 24.8 + - - -
449C GLU* 4.9 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 589 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B LYS 5.3 0.7 - - - -
523B ALA* 2.6 39.5 + - - +
525B GLN* 5.5 2.1 + - - +
585B GLU 2.9 20.5 + - - -
586B ILE* 3.5 4.3 - - - +
588B GLU* 1.3 74.4 - - - +
590B CYS* 1.3 58.9 + - - +
593B LYS* 3.5 12.0 - - - +
594B LEU* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 590 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B ALA* 3.9 14.4 - - + +
524B CYS* 3.9 15.7 - - - -
558B LEU* 4.2 9.6 - - + -
562B VAL* 3.4 42.6 - - - -
586B ILE* 2.8 31.8 + - + +
589B SER* 1.3 72.6 + - - +
591B VAL* 1.3 67.2 + - + +
592B CYS 3.4 0.3 + - - -
594B LEU* 3.4 4.2 + - - +
595B MET* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il